RUcore: Rutgers University Community Repository
A framework for replica exchange simulations
Descriptive
TitleInfo
Title
A framework for replica exchange simulations
Name
(type = personal)
NamePart
(type = family)
Treikalis
NamePart
(type = given)
Antons
NamePart
(type = date)
1982-
DisplayForm
Antons Treikalis
Role
RoleTerm
(authority = RULIB)
author
Name
(type = personal)
NamePart
(type = family)
Jha
NamePart
(type = given)
Shantenu
DisplayForm
Shantenu Jha
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
York
NamePart
(type = given)
Darrin
DisplayForm
Darrin York
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Dehnavi
NamePart
(type = given)
Maryam Mehri
DisplayForm
Maryam Mehri Dehnavi
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = corporate)
NamePart
Rutgers University
Role
RoleTerm
(authority = RULIB)
degree grantor
Name
(type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm
(authority = RULIB)
school
TypeOfResource
Text
Genre
(authority = marcgt)
theses
OriginInfo
DateCreated
(qualifier = exact)
2017
DateOther
(qualifier = exact);
(type = degree)
2017-05
CopyrightDate
(encoding = w3cdtf);
(qualifier = exact)
2017
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
(authority = ISO639-2b);
(type = code)
eng
Abstract
(type = abstract)
Replica Exchange (RE) simulations have emerged as an important algorithmic tool for the molecular sciences. Typically RE functionality is integrated into the molecular simulation soft- ware package. A primary motivation for the tight integration of RE functionality with sim- ulation codes has been performance. This is limiting at multiple levels. First, advances in the RE methodology are tied to the molecular simulation code for which they were developed. Second, it is difficult to extend or experiment with various RE methods, since expertise in the molecular simulation code is required. We propose the RepEx framework which addresses the aforementioned limitations, while striking the balance between flexibility (RE pattern) and scalability (several thousand replicas) over a diverse range of HPC platforms. In this thesis is introduced the RepEx framework, the primary contributions of which are: (i) its ability to support different RE patterns independent of molecular simulation codes, (ii) the ability to execute different exchange types and replica counts independent of the specific availability of resources, (iii) a runtime system that has first-class support for task- level parallelism, and (iv) provide the required scalability along multiple dimensions.
Subject
(authority = RUETD)
Topic
Electrical and Computer Engineering
RelatedItem
(type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier
(type = RULIB)
ETD
Identifier
ETD_7922
PhysicalDescription
Form
(authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
1 online resource (iv, 93 p. : ill.)
Note
(type = degree)
M.S.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Antons Treikalis
RelatedItem
(type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier
(type = local)
rucore19991600001
Location
PhysicalLocation
(authority = marcorg);
(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3PN98JR
Genre
(authority = ExL-Esploro)
ETD graduate
Back to the top
Rights
RightsDeclaration
(ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder
(type = personal)
Name
FamilyName
Treikalis
GivenName
Antons
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
(encoding = w3cdtf);
(qualifier = exact);
(point = start)
2017-04-02 13:20:07
AssociatedEntity
Name
Antons Treikalis
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
Back to the top
Technical
RULTechMD
(ID = TECHNICAL1)
ContentModel
ETD
OperatingSystem
(VERSION = 5.1)
windows xp
CreatingApplication
Version
1.5
ApplicationName
pdfTeX-1.40.14
DateCreated
(point = end);
(encoding = w3cdtf);
(qualifier = exact)
2017-04-25T22:39:48
DateCreated
(point = end);
(encoding = w3cdtf);
(qualifier = exact)
2017-04-25T22:39:48
Back to the top
Statistical Profile